How is the account set up in Thunderbird, as POP or IMAP? Find out using menu path Tools->Account Settings->Server Settings->Server Type at the top right of the dialogue.

First backup your profile -- http://kb.mozillazine.org/Profile_backupRight click on the name of the folder in which you find this happening. From the context menu that appears, click on "Properties" then on "Repair folder" in the next dialogue.